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- PDB-7uk2: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 7uk2
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with NN-390
ComponentsHdac6 protein
KeywordsMETAL BINDING PROTEIN/INHIBITOR / potassium ion binding / alkali metal ion binding / ion binding / cation binding / metal ion binding / catalytic activity / hydrolase activity / deacetylase activity / protein deacetylase activity / acting on a protein / acting on carbon-nitrogen (but not peptide) bonds / in linear amides / tubulin deacetylase activity / zinc ion binding / transition metal ion binding / METAL BINDING PROTEIN / METAL BINDING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


swimming behavior / tubulin deacetylase activity / definitive hemopoiesis / protein lysine deacetylase activity / regulation of tubulin deacetylation / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / epigenetic regulation of gene expression ...swimming behavior / tubulin deacetylase activity / definitive hemopoiesis / protein lysine deacetylase activity / regulation of tubulin deacetylation / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / epigenetic regulation of gene expression / angiogenesis / zinc ion binding
Similarity search - Function
Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / Chem-O2L / Hdac6 protein
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsErdogan, F. / Seo, H.-S. / Dhe-Paganon, S.
Funding support Canada, 5items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2014-05767 Canada
Canadian Institutes of Health Research (CIHR)MOP-130424 Canada
Canada Research Chairs950-232042 Canada
Ontario Research Fund34876 Canada
Canada Foundation for Innovation33536 Canada
Citation
Journal: Pharmaceuticals / Year: 2022
Title: High Efficacy and Drug Synergy of HDAC6-Selective Inhibitor NN-429 in Natural Killer (NK)/T-Cell Lymphoma.
Authors: Garcha, H.K. / Nawar, N. / Sorger, H. / Erdogan, F. / Aung, M.M.K. / Sedighi, A. / Manaswiyoungkul, P. / Seo, H.S. / Schonefeldt, S. / Poloske, D. / Dhe-Paganon, S. / Neubauer, H.A. / ...Authors: Garcha, H.K. / Nawar, N. / Sorger, H. / Erdogan, F. / Aung, M.M.K. / Sedighi, A. / Manaswiyoungkul, P. / Seo, H.S. / Schonefeldt, S. / Poloske, D. / Dhe-Paganon, S. / Neubauer, H.A. / Mustjoki, S.M. / Herling, M. / de Araujo, E.D. / Moriggl, R. / Gunning, P.T.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: J Med Chem / Year: 2021
Title: Unique Molecular Interaction with the Histone Deacetylase 6 Catalytic Tunnel: Crystallographic and Biological Characterization of a Model Chemotype.
Authors: Olaoye, O.O. / Watson, P.R. / Nawar, N. / Geletu, M. / Sedighi, A. / Bukhari, S. / Raouf, Y.S. / Manaswiyoungkul, P. / Erdogan, F. / Abdeldayem, A. / Cabral, A.D. / Hassan, M.M. / Toutah, K. ...Authors: Olaoye, O.O. / Watson, P.R. / Nawar, N. / Geletu, M. / Sedighi, A. / Bukhari, S. / Raouf, Y.S. / Manaswiyoungkul, P. / Erdogan, F. / Abdeldayem, A. / Cabral, A.D. / Hassan, M.M. / Toutah, K. / Shouksmith, A.E. / Gawel, J.M. / Israelian, J. / Radu, T.B. / Kachhiyapatel, N. / de Araujo, E.D. / Christianson, D.W. / Gunning, P.T.
History
DepositionMar 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2895
Polymers39,7251
Non-polymers5644
Water6,882382
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.263, 83.135, 93.276
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1193-

HOH

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Components

#1: Protein Hdac6 protein / Histone Deacetylase 6


Mass: 39724.973 Da / Num. of mol.: 1 / Fragment: catalytic domain 2 (UNP residues 290-646)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli (E. coli) / References: UniProt: A7YT55
#2: Chemical ChemComp-O2L / N-hydroxy-4-{[(propan-2-yl)(2,3,4,5-tetrafluorobenzene-1-sulfonyl)amino]methyl}benzamide


Mass: 420.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16F4N2O4S / Details: NN-390 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 12% PEG3350, 0.2M Potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→93.28 Å / Num. obs: 53466 / % possible obs: 99.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 15.67 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.268 / Rpim(I) all: 0.118 / Rrim(I) all: 0.293 / Net I/σ(I): 8 / Num. measured all: 330695
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.625.81.1251417024320.5940.4971.2341.792.5
8.74-93.285.20.09420483970.9910.0450.10517.899.7

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
xia2data scaling
PHASERphasing
PDB_EXTRACTdata extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6csr

6csr


Resolution: 1.6→62.06 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2215 2637 4.94 %
Rwork0.1985 50748 -
obs0.1996 53385 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.47 Å2 / Biso mean: 18.0627 Å2 / Biso min: 4.7 Å2
Refinement stepCycle: final / Resolution: 1.6→62.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 31 382 3169
Biso mean--25.15 30.75 -
Num. residues----353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.630.41421410.34862412255392
1.63-1.660.34741530.306426592812100
1.66-1.690.32331290.279126522781100
1.69-1.730.30421370.258626352772100
1.73-1.770.31461670.24726212788100
1.77-1.810.25921380.232526562794100
1.81-1.860.24481270.220526582785100
1.86-1.920.25281310.21226642795100
1.92-1.980.25651330.22222652278599
1.98-2.050.22481520.225526682820100
2.05-2.130.24471380.195326722810100
2.13-2.230.20611290.192826682797100
2.23-2.340.2241080.188726832791100
2.34-2.490.22311390.197526802819100
2.49-2.680.21631660.191526782844100
2.68-2.950.22081360.192827132849100
2.95-3.380.20211260.186727342860100
3.38-4.260.17721380.16172762290099
4.26-62.060.16811490.168628813030100

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